Differential DNA Methylation of Networked Signaling, Transcriptional, Innate and Adaptive Immunity, and Osteoclastogenesis Genes and Pathways in Gout

Abstract

Objective. In gout, autoinflammatory responses to urate crystals promote acute arthritis flares, but the pathogeneses of tophi, chronic synovitis, and erosion are less well understood. Defining the pathways of epigenomic immunity training can reveal novel pathogenetic factors and biomarkers. The present study was undertaken to seminally probe differential DNA methylation patterns utilizing epigenome-wide analyses in patients with gout.Methods. Peripheral blood mononuclear cells (PBMCs) were obtained from a San Diego cohort of patients with gout (n = 16) and individually matched healthy controls (n = 14). PBMC methylome data were processed with ChAMP package in R. ENCODE data and Taiji data analysis software were used to analyze transcription factor (TF)-gene networks. As an independent validation cohort, whole blood DNA samples from New Zealand Māori subjects (n = 13 patients with gout, n = 16 control subjects without gout) were analyzed.Results. Differentially methylated loci clearly separated gout patients from controls, as determined by hierarchical clustering and principal components analyses. IL23R, which mediates granuloma formation and cell invasion, was identified as one of the multiple differentially methylated gout risk genes. Epigenome-wide analyses revealed differential methylome pathway enrichment for B and T cell receptor signaling, Th17 cell differentiation and interleukin-17 signaling, convergent longevity regulation, circadian entrainment, and AMP-activated protein kinase signaling, which are pathways that impact inflammation via insulin-like growth factor 1 receptor, phosphatidylinositol 3-kinase/Akt, NF-κB, mechanistic target of rapamycin signaling, and autophagy. The gout cohorts overlapped for 37 (52.9%) of the 70 TFs with hypomethylated sequence enrichment and for 30 (78.9%) of the 38 enriched KEGG pathways identified via TFs. Evidence of shared differentially methylated gout TF-gene networks, including the NF-κB activation-limiting TFs MEF2C and NFATC2, pointed to osteoclast differentiation as the most strongly weighted differentially methylated pathway that overlapped in both gout cohorts.Conclusion. These findings of differential DNA methylation of networked signaling, transcriptional, innate and adaptive immunity, and osteoclastogenesis genes and pathways suggest that they could serve as novel therapeutic targets in the management of flares, tophi, chronic synovitis, and bone erosion in patients with gout.

Monosodium Urate Crystals regulate a unique JNK-dependent macrophage metabolic and inflammatory response

“…Our data from mouse has clinical implications since we demonstrated that individuals with gout display lower levels of blood glucose levels when compared to those with HU but not gout. Moreover, prior studies have shown 75 transcription factor motifs associated with hypomethylated differential methylation loci regions in gout vs. healthy controls (48) including those that belong to MEF2C, NFATC2, JUN and FOS, HIF1A, MYC-MAX and circadian clock regulators CLOCK and BHLHLE40. Interestingly, we find upregulation of Fosb, Fosl1, Fosl2, Hif1a, Max and Bhlhe40 -but not Mef2c that was downregulated or Nfatc2 that was unaffected-in PBMC from mice injected with MSUc indicating that similar signaling pathways might be involved in the activation of PBMC in patients with gout during flares.…”

The Roles of Epigenetics Regulation in Bone Metabolism and Osteoporosis

“…DNA methylation sequencing further confirmed that the promoter regions of Runx2 and OSX exhibited significantly decreased DNA methylation levels, and the DNA methylation levels were significantly correlated with gene expression (Zhang R. P. et al, 2011). Inhibition of FIGURE 2 | Molecular mechanism of DNA methylation (Yang and Duan, 2016;Letarouilly et al, 2019;Ahmed et al, 2020;Wang et al, 2020;Xu et al, 2020). DNA methylation modification is mainly controlled by DNMT proteins.…”

“… Molecular mechanism of DNA methylation ( Yang and Duan, 2016 ; Letarouilly et al, 2019 ; Ahmed et al, 2020 ; Wang et al, 2020 ; Xu et al, 2020 ). DNA methylation modification is mainly controlled by DNMT proteins.…”

“…Four known DNMT subtypes (DNMT1, DNMT3a, DNMT3b, and DNMT3L) exist in mammalian cells, the first three of which are active DNMTs ( Ahmed et al, 2020 ; Wang et al, 2020 ). The major DNA methylation inhibitors can be divided into two broad classes: nucleoside analogies, such as 5-aza-2’-deoxycytidine (5-Aza-dC) and 5-Aza-C, and non-nucleoside analogs, including procaine, homocysteine (Hcys).…”

Regulatory T cells induced by B cells suppress NLRP3 inflammasome activation and alleviate monosodium urate-induced gouty inflammation

“…Gouty inflammation is an acute and painful type of arthritis caused by the precipitation of monosodium urate (MSU) in the joints. The phagocytosis of MSU by macrophages triggers NLRP3 inflammasome activation, resulting in secretion of IL-1β which plays a key role in the inflammatory cascade ( Bach et al., 2019 ; Kingsbury et al., 2011 ; Liu-Bryan, 2010 ; Shin et al., 2019 ; Steiger and Harper, 2014 ; Wang et al., 2020 ). In addition, MSU could directly activate T cells in an antigen-independent manner in gouty arthritis ( Webb et al., 2009 ).…”